def phenix_prep(xyzin, phenix_tlsin_list, phenix_tlsout):
"""PHENIX input file. Tells 'phenix.refine' what the TLS groups are.
"""
## load structure
struct = FileIO.LoadStructure(fil=xyzin)
## load and construct TLS groups
tls_group_list = []
tls_file = TLS.TLSFile()
tls_file.set_file_format(TLS.TLSFileFormatPHENIX())
tls_file_format = TLS.TLSFileFormatPHENIX()
for tlsin in phenix_tlsin_list:
tls_desc_list = tls_file_format.load(open(tlsin, "r"))
for tls_desc in tls_desc_list:
tls_file.tls_desc_list.append(tls_desc)
tls_group = tls_desc.construct_tls_group_with_atoms(struct)
tls_group.tls_desc = tls_desc
tls_group_list.append(tls_group)
## now save the PHENIX file in phenix.refine format
tls_file.save(open(phenix_tlsout, "w"))
